This is an R Markdown Notebook. When you execute code within the notebook, the results appear beneath the code.

Try executing this chunk by clicking the Run button within the chunk or by placing your cursor inside it and pressing Ctrl+Shift+Enter.

load dataset

ctrl_filtered <- readRDS("./processed_data_file/ctrl_filtered.rds")
HSD_filtered <- readRDS("./processed_data_file/HSD_filtered.rds")
umapplot(ctrl_filtered, group.by = "ref_celltype")
Scale for 'colour' is already present. Adding another scale for 'colour', which will
replace the existing scale.

umapplot(HSD_filtered, group.by = "ref_celltype")
Scale for 'colour' is already present. Adding another scale for 'colour', which will
replace the existing scale.

scmap

ref_sce <- mkref_scmap_from_seuobj(ctrl_filtered)
Parameter M was not provided, will use M = n_features / 10 (if n_features <= 1000), where n_features is the number of selected features, and M = 100 otherwise.
Parameter k was not provided, will use k = sqrt(number_of_cells)
HSD_filtered <- query_scmap_from_refsce(HSD_filtered, ref_sce, ref_labels = 'celltype')
Parameter M was not provided, will use M = n_features / 10 (if n_features <= 1000), where n_features is the number of selected features, and M = 100 otherwise.
Parameter k was not provided, will use k = sqrt(number_of_cells)
umapplot(HSD_filtered,group.by = "scmap_idents")
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the
existing scale.

prop_confuse_mat
     
               ASP           DB           DT           SB           PC           TC           VB
  ASP 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
  DB  0.0000000000 0.9623103279 0.0110732538 0.0000000000 0.0320699708 0.0000000000 0.0163487738
  DT  0.0000000000 0.0063631914 0.9514480409 0.0064516129 0.0029154519 0.0000000000 0.0000000000
  SB  0.0000000000 0.0004894763 0.0144804089 0.9935483871 0.0029154519 0.0370370370 0.0000000000
  PC  0.0000000000 0.0181106216 0.0000000000 0.0000000000 0.9620991254 0.0000000000 0.0000000000
  TC  0.0000000000 0.0000000000 0.0212947189 0.0000000000 0.0000000000 0.9629629630 0.0000000000
  VB  0.0000000000 0.0073421439 0.0008517888 0.0000000000 0.0000000000 0.0000000000 0.9700272480
  LT  0.0000000000 0.0053842389 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0136239782
  GB  0.0000000000 0.0000000000 0.0008517888 0.0000000000 0.0000000000 0.0000000000 0.0000000000
     
                LT           GB
  ASP 0.0000000000 0.0000000000
  DB  0.0000000000 0.0000000000
  DT  0.0092592593 0.0000000000
  SB  0.0000000000 0.0000000000
  PC  0.0000000000 0.0000000000
  TC  0.0000000000 0.0000000000
  VB  0.0000000000 0.0000000000
  LT  0.9907407407 0.0000000000
  GB  0.0000000000 1.0000000000

Add a new chunk by clicking the Insert Chunk button on the toolbar or by pressing Ctrl+Alt+I.

When you save the notebook, an HTML file containing the code and output will be saved alongside it (click the Preview button or press Ctrl+Shift+K to preview the HTML file).

The preview shows you a rendered HTML copy of the contents of the editor. Consequently, unlike Knit, Preview does not run any R code chunks. Instead, the output of the chunk when it was last run in the editor is displayed.

LS0tCnRpdGxlOiAiUiBOb3RlYm9vayIKb3V0cHV0OiBodG1sX25vdGVib29rCi0tLQoKVGhpcyBpcyBhbiBbUiBNYXJrZG93bl0oaHR0cDovL3JtYXJrZG93bi5yc3R1ZGlvLmNvbSkgTm90ZWJvb2suIFdoZW4geW91IGV4ZWN1dGUgY29kZSB3aXRoaW4gdGhlIG5vdGVib29rLCB0aGUgcmVzdWx0cyBhcHBlYXIgYmVuZWF0aCB0aGUgY29kZS4gCgpUcnkgZXhlY3V0aW5nIHRoaXMgY2h1bmsgYnkgY2xpY2tpbmcgdGhlICpSdW4qIGJ1dHRvbiB3aXRoaW4gdGhlIGNodW5rIG9yIGJ5IHBsYWNpbmcgeW91ciBjdXJzb3IgaW5zaWRlIGl0IGFuZCBwcmVzc2luZyAqQ3RybCtTaGlmdCtFbnRlciouIAoKYGBge3Igc2V0dXAsIGluY2x1ZGU9RkFMU0V9CmdldHdkKCkKa25pdHI6Om9wdHNfa25pdCRzZXQocm9vdC5kaXIgPSAiL2hvbWUvemp1L3RpYW5mZW5nL3NpbmdsZV9jZWxsX2F0bGFzIikKIyBzZXR3ZCgiL2hvbWUvemp1L3RpYW5mZW5nL3NpbmdsZV9jZWxsX2F0bGFzIikKIyBnZXR3ZCgpCmBgYAoKYGBge3J9CnNvdXJjZSgiLi91dGlscy90aWFuZmVuZ1J3cmFwcGVycy5SIikKc291cmNlKCIuL3V0aWxzL1hHQm9vc3Rfd3JhcHBlci5SIikKYGBgCgojIGxvYWQgZGF0YXNldApgYGB7cn0KY3RybF9maWx0ZXJlZCA8LSByZWFkUkRTKCIuL3Byb2Nlc3NlZF9kYXRhX2ZpbGUvY3RybF9maWx0ZXJlZC5yZHMiKQpIU0RfZmlsdGVyZWQgPC0gcmVhZFJEUygiLi9wcm9jZXNzZWRfZGF0YV9maWxlL0hTRF9maWx0ZXJlZC5yZHMiKQpgYGAKCgpgYGB7cn0KIyBzZWxlY3RlZF9mZWF0dXJlcyA8LWludGVyc2VjdChGaW5kVmFyaWFibGVGZWF0dXJlcyhkczEsIG5mZWF0dXJlcyA9IDIwMClAYXNzYXlzW1siU0NUIl1dQHZhci5mZWF0dXJlcywKIyAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICBGaW5kVmFyaWFibGVGZWF0dXJlcyhkczIsIG5mZWF0dXJlcyA9IDIwMClAYXNzYXlzW1siU0NUIl1dQHZhci5mZWF0dXJlcykgJT4lCiMgICBpbnRlcnNlY3QoRmluZFZhcmlhYmxlRmVhdHVyZXMoZHMwLCBuZmVhdHVyZXMgPSAyMDApQGFzc2F5c1tbIlNDVCJdXUB2YXIuZmVhdHVyZXMpCgojIyBjdHJs5L2c5Li6cmVmCiMjIOS/ruaUueagh+etvuS4uuaVsOWtl++8jOa3u+WKoOagh+etvuaYoOWwhApjdHJsX2ZpbHRlcmVkJGNlbGx0eXBlIDwtIGRyb3BsZXZlbHMoY3RybF9maWx0ZXJlZCRjZWxsdHlwZSkKSFNEX2ZpbHRlcmVkJGNlbGx0eXBlIDwtIGRyb3BsZXZlbHMoSFNEX2ZpbHRlcmVkJGNlbGx0eXBlKQoKY3RybF9maWx0ZXJlZCR4Z2Jvb3N0X2xhYmVsIDwtIGN0cmxfZmlsdGVyZWQkY2VsbHR5cGUKbGV2ZWxzKGN0cmxfZmlsdGVyZWQkeGdib29zdF9sYWJlbCkgPC0gbGV2ZWxzKGN0cmxfZmlsdGVyZWQkY2VsbHR5cGUpICU+JSBsZW5ndGgoKSAlPiUgc2VxKC4pLTEKSWRlbnRzKGN0cmxfZmlsdGVyZWQpIDwtIGN0cmxfZmlsdGVyZWQkeGdib29zdF9sYWJlbAoKSFNEX2ZpbHRlcmVkJHhnYm9vc3RfbGFiZWwgPC0gSFNEX2ZpbHRlcmVkJGNlbGx0eXBlCmxldmVscyhIU0RfZmlsdGVyZWQkeGdib29zdF9sYWJlbCkgPC0gbGV2ZWxzKEhTRF9maWx0ZXJlZCRjZWxsdHlwZSkgJT4lIGxlbmd0aCgpICU+JSBzZXEoLiktMQpJZGVudHMoSFNEX2ZpbHRlcmVkKSA8LSBIU0RfZmlsdGVyZWQkeGdib29zdF9sYWJlbAoKYnN0X21vZGVsIDwtIFhHQm9vc3RfdHJhaW5fZnJvbV9zZXVvYmooY3RybF9maWx0ZXJlZCkKSFNEX2ZpbHRlcmVkIDwtIFhHQm9vc3RfcHJlZGljdF9mcm9tX3NldW9iaihIU0RfZmlsdGVyZWQsIGJzdF9tb2RlbCkKSFNEX2ZpbHRlcmVkIDwtIHByb2plY3QycmVmX2NlbGx0eXBlKEhTRF9maWx0ZXJlZCwgY3RybF9maWx0ZXJlZCwgcmVmX2xhYmVscyA9IGMoInhnYm9vc3RfbGFiZWwiLCJjZWxsdHlwZSIpKQoKY3RybF9maWx0ZXJlZCA8LSBYR0Jvb3N0X3ByZWRpY3RfZnJvbV9zZXVvYmooY3RybF9maWx0ZXJlZCwgYnN0X21vZGVsKQpjdHJsX2ZpbHRlcmVkIDwtIHByb2plY3QycmVmX2NlbGx0eXBlKGN0cmxfZmlsdGVyZWQsIGN0cmxfZmlsdGVyZWQsIHJlZl9sYWJlbHMgPSBjKCJ4Z2Jvb3N0X2xhYmVsIiwiY2VsbHR5cGUiKSkKCiMgSWRlbnRzKGRzMikgPC0gZHMyJENsYXNzaWZpY2F0aW9uMQojIHJlZl9zY2UgPC0gbWtyZWZfc2NtYXBfZnJvbV9zZXVvYmooZHMyKQojIGRzMSA8LSBxdWVyeV9zY21hcF9mcm9tX3JlZnNjZShkczEsIHJlZl9zY2UpCiMgZHMwIDwtIHF1ZXJ5X3NjbWFwX2Zyb21fcmVmc2NlKGRzMCwgcmVmX3NjZSkKCnVtYXBwbG90KGN0cmxfZmlsdGVyZWQsIGdyb3VwLmJ5ID0gInJlZl9jZWxsdHlwZSIpCnVtYXBwbG90KEhTRF9maWx0ZXJlZCwgZ3JvdXAuYnkgPSAicmVmX2NlbGx0eXBlIikKCiMgdW1hcHBsb3QoZHMxLCBncm91cC5ieSA9ICJzY21hcF9pZGVudHMiKQojIHVtYXBwbG90KGRzMCwgZ3JvdXAuYnkgPSAic2NtYXBfaWRlbnRzIikKYGBgCmBgYHtyfQpjb25mdXNlX21hdCA8LSBYR0Jvb3N0X3ByZWRpY3RfZnJvbV9zZXVvYmooSFNEX2ZpbHRlcmVkLCBic3RfbW9kZWwsIHJldHVybl9jb25mdXNlX21hdHJpeCA9IFQpCgpsYWJlbDEgPSBkaW1uYW1lcyhjb25mdXNlX21hdCkkcHJlCmxhYmVsMiA9IGRpbW5hbWVzKGNvbmZ1c2VfbWF0KSR0cnVlCgpjb25mdXNlX21hdCA8LSBjb25mdXNlX21hdFttYXRjaChsYWJlbDIsbGFiZWwxKSxdCgpzb3VyY2VzIDwtIHJlcCgwOihsZW5ndGgobGFiZWwxKSAtIDEpLCBlYWNoID0gbGVuZ3RoKGxhYmVsMikpICMg5rOo5oSP6L+Z6YeM55qEZWFjaOWSjHRpbWVz55qE5Yy65YirCmNvbG9ycyA8LSByZXAoYWVyb19jb2xvcnNfbGlzdFtjKDE6OSldLCBlYWNoID0gbGVuZ3RoKGxhYmVsMikpCnRhcmdldHMgPC0gcmVwKGxlbmd0aChsYWJlbDEpICsgMDoobGVuZ3RoKGxhYmVsMikgLSAxKSwgdGltZXMgPSBsZW5ndGgobGFiZWwxKSkKCnBsb3RfbHkoCiAgICB0eXBlID0gInNhbmtleSIsIG9yaWVudGF0aW9uID0gImgiLAogICAgbm9kZSA9IGxpc3QoCiAgICAgICAgbGFiZWwgPSBjKGxldmVscyhjdHJsX2ZpbHRlcmVkJGNlbGx0eXBlKSwidW5hc3NpZ25lZCIsbGV2ZWxzKEhTRF9maWx0ZXJlZCRjZWxsdHlwZSkpLAogICAgICAgIGNvbG9yID0gYyhjb2xvcnNfbGlzdFtjKDE6OSldLCAiYmxhY2siLGNvbG9yc19saXN0W2MoMTo5KV0pLCBwYWQgPSAxNSwgdGhpY2tuZXNzID0gMzAsCiAgICAgICAgbGluZSA9IGxpc3QoY29sb3IgPSAiYmxhY2siLCB3aWR0aCA9IDEpCiAgICApLAogICAgbGluayA9IGxpc3QoCiAgICAgICAgc291cmNlID0gc291cmNlcywgdGFyZ2V0ID0gdGFyZ2V0cywKICAgICAgICB2YWx1ZSA9IGFzLm51bWVyaWMoY29uZnVzZV9tYXQpLAogICAgICAgIGNvbG9yID0gY29sb3JzCiAgICApCikgJT4lIGxheW91dCh0aXRsZSA9ICJDdHJsIGFzIHJlZiIsIGZvbnQgPSBsaXN0KGZhbWlseSA9ICJBcmlhbCIsIHNpemUgPSAyMCwgY29sb3IgPSAiYmxhY2siKSkKYGBgCgojIHNjbWFwCmBgYHtyfQpyZWZfc2NlIDwtIG1rcmVmX3NjbWFwX2Zyb21fc2V1b2JqKGN0cmxfZmlsdGVyZWQpCkhTRF9maWx0ZXJlZCA8LSBxdWVyeV9zY21hcF9mcm9tX3JlZnNjZShIU0RfZmlsdGVyZWQsIHJlZl9zY2UsIHJlZl9sYWJlbHMgPSAnY2VsbHR5cGUnKQpgYGAKCgpgYGB7cn0KdW1hcHBsb3QoSFNEX2ZpbHRlcmVkLGdyb3VwLmJ5ID0gInNjbWFwX2lkZW50cyIpCmBgYApgYGB7cn0KY29uZnVzZV9tYXQgPC0gdGFibGUoSFNEX2ZpbHRlcmVkJHNjbWFwX2lkZW50cyxIU0RfZmlsdGVyZWQkY2VsbHR5cGUpCmxhYmVsMSA9IGRpbW5hbWVzKGNvbmZ1c2VfbWF0KVtbMV1dCmxhYmVsMiA9IGRpbW5hbWVzKGNvbmZ1c2VfbWF0KVtbMl1dCgpjb25mdXNlX21hdCA8LSBjb25mdXNlX21hdFttYXRjaChsYWJlbDIsbGFiZWwxKSxdCmxhYmVsMSA9IGRpbW5hbWVzKGNvbmZ1c2VfbWF0KVtbMV1dCmxhYmVsMiA9IGRpbW5hbWVzKGNvbmZ1c2VfbWF0KVtbMl1dCgpjb25mdXNlX21hdDIgPC0gY29uZnVzZV9tYXQgLSBkaWFnKGRpYWcoY29uZnVzZV9tYXQpKQpwcm9wX2NvbmZ1c2VfbWF0MiA8LSBwcm9wX2NvbmZ1c2VfbWF0IC0gZGlhZyhkaWFnKHByb3BfY29uZnVzZV9tYXQpKQoKc291cmNlcyA8LSByZXAoMDoobGVuZ3RoKGxhYmVsMSkgLSAxKSwgZWFjaCA9IGxlbmd0aChsYWJlbDIpKSAjIOazqOaEj+i/memHjOeahGVhY2jlkox0aW1lc+eahOWMuuWIqwpjb2xvcnMgPC0gcmVwKGFlcm9fY29sb3JzX2xpc3RbYygxOjkpXSwgZWFjaCA9IGxlbmd0aChsYWJlbDIpKQp0YXJnZXRzIDwtIHJlcChsZW5ndGgobGFiZWwxKSArIDA6KGxlbmd0aChsYWJlbDIpIC0gMSksIHRpbWVzID0gbGVuZ3RoKGxhYmVsMSkpCgpwbG90X2x5KAogICAgdHlwZSA9ICJzYW5rZXkiLCBvcmllbnRhdGlvbiA9ICJoIiwKICAgIG5vZGUgPSBsaXN0KAogICAgICAgIGxhYmVsID0gYyhsYWJlbDIsbGFiZWwyKSwKICAgICAgICBjb2xvciA9IGMoY29sb3JzX2xpc3RbYygxOjkpXSwgImJsYWNrIixjb2xvcnNfbGlzdFtjKDE6OSldKSwgcGFkID0gMTUsIHRoaWNrbmVzcyA9IDMwLAogICAgICAgIGxpbmUgPSBsaXN0KGNvbG9yID0gImJsYWNrIiwgd2lkdGggPSAxKQogICAgKSwKICAgIGxpbmsgPSBsaXN0KAogICAgICAgIHNvdXJjZSA9IHNvdXJjZXMsIHRhcmdldCA9IHRhcmdldHMsCiAgICAgICAgdmFsdWUgPSBhcy5udW1lcmljKHByb3BfY29uZnVzZV9tYXQpLAogICAgICAgIGNvbG9yID0gY29sb3JzCiAgICApCikgJT4lIGxheW91dCh0aXRsZSA9ICJDdHJsIGFzIHJlZiIsIGZvbnQgPSBsaXN0KGZhbWlseSA9ICJBcmlhbCIsIHNpemUgPSAyMCwgY29sb3IgPSAiYmxhY2siKSkKYGBgCmBgYHtyfQpwcm9wX2NvbmZ1c2VfbWF0IDwtIHByb3AudGFibGUoY29uZnVzZV9tYXQsbWFyZ2luID0gMSkKcHJvcF9jb25mdXNlX21hdDIKYGBgCgpBZGQgYSBuZXcgY2h1bmsgYnkgY2xpY2tpbmcgdGhlICpJbnNlcnQgQ2h1bmsqIGJ1dHRvbiBvbiB0aGUgdG9vbGJhciBvciBieSBwcmVzc2luZyAqQ3RybCtBbHQrSSouCgpXaGVuIHlvdSBzYXZlIHRoZSBub3RlYm9vaywgYW4gSFRNTCBmaWxlIGNvbnRhaW5pbmcgdGhlIGNvZGUgYW5kIG91dHB1dCB3aWxsIGJlIHNhdmVkIGFsb25nc2lkZSBpdCAoY2xpY2sgdGhlICpQcmV2aWV3KiBidXR0b24gb3IgcHJlc3MgKkN0cmwrU2hpZnQrSyogdG8gcHJldmlldyB0aGUgSFRNTCBmaWxlKS4KClRoZSBwcmV2aWV3IHNob3dzIHlvdSBhIHJlbmRlcmVkIEhUTUwgY29weSBvZiB0aGUgY29udGVudHMgb2YgdGhlIGVkaXRvci4gQ29uc2VxdWVudGx5LCB1bmxpa2UgKktuaXQqLCAqUHJldmlldyogZG9lcyBub3QgcnVuIGFueSBSIGNvZGUgY2h1bmtzLiBJbnN0ZWFkLCB0aGUgb3V0cHV0IG9mIHRoZSBjaHVuayB3aGVuIGl0IHdhcyBsYXN0IHJ1biBpbiB0aGUgZWRpdG9yIGlzIGRpc3BsYXllZC4=